knitr document van Steensel lab
TF reporter barcode processing - pMT02 - stimulation 2
Introduction
18,000 TF reporters on pMT02 were transfected into mESCs (in total 10 different conditions), sequencing data yielded barcode counts of these experiments. These counts will be processed in this script.
Analysis
Add barcode annotation to barcode counts & extract first bc read count information
Data quality plots
Normalization of barcode counts:
Divide cDNA barcode counts through pDNA barcode counts to get activity
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## [1] "progress: 100 %"Calculate mean activity - filter out outlier barcodes
Calculate correlations between technical replicates
Data quality plots - correlation between replicates
Session Info
## [1] "Run time: 8.483114 mins"## [1] "/DATA/usr/m.trauernicht/projects/SuRE-TF/gen-1_stimulation-2"## [1] "Thu Nov 26 09:42:59 2020"## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.7 LTS
##
## Matrix products: default
## BLAS: /usr/lib/libblas/libblas.so.3.6.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] gridExtra_2.3 RColorBrewer_1.1-2 readr_1.3.1
## [4] haven_2.2.0 ggbeeswarm_0.6.0 plotly_4.9.2.1
## [7] tibble_3.0.1 dplyr_0.8.5 vwr_0.3.0
## [10] latticeExtra_0.6-29 lattice_0.20-38 stringdist_0.9.5.5
## [13] GGally_1.5.0 ggpubr_0.2.5 magrittr_1.5
## [16] ggplot2_3.3.0 stringr_1.4.0 plyr_1.8.6
## [19] data.table_1.12.8
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.5 tidyr_1.0.0 png_0.1-7 assertthat_0.2.1
## [5] digest_0.6.27 mime_0.9 R6_2.5.0 evaluate_0.14
## [9] httr_1.4.1 pillar_1.4.3 rlang_0.4.8 lazyeval_0.2.2
## [13] Matrix_1.2-18 rmarkdown_2.5 splines_3.6.3 labeling_0.3
## [17] htmlwidgets_1.5.2 munsell_0.5.0 shiny_1.4.0 compiler_3.6.3
## [21] vipor_0.4.5 httpuv_1.5.4 xfun_0.19 pkgconfig_2.0.3
## [25] mgcv_1.8-31 htmltools_0.5.0 tidyselect_1.1.0 reshape_0.8.8
## [29] viridisLite_0.3.0 later_1.1.0.1 crayon_1.3.4 withr_2.1.2
## [33] grid_3.6.3 nlme_3.1-143 xtable_1.8-4 jsonlite_1.7.1
## [37] gtable_0.3.0 lifecycle_0.2.0 scales_1.1.0 stringi_1.5.3
## [41] farver_2.0.1 ggsignif_0.6.0 reshape2_1.4.4 promises_1.1.1
## [45] ellipsis_0.3.0 vctrs_0.2.4 tools_3.6.3 forcats_0.4.0
## [49] glue_1.4.2 beeswarm_0.2.3 purrr_0.3.3 hms_0.5.3
## [53] crosstalk_1.0.0 jpeg_0.1-8.1 prettydoc_0.4.0 fastmap_1.0.1
## [57] yaml_2.2.1 colorspace_1.4-1 knitr_1.30